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Statistics of Affymetrix and Custom CDF Files (Version 10)

Table 1: Probe utilization

Species	Chip	Probe count	UG (%)	REFSEQ (%)	ENTREZG (%)	ENSG (%)	ENST (%)	ENSE (%)	VEGAG (%)	VEGAT (%)	VEGAE (%)	TAIR (%)
Arabidopsis thaliana	AtGenome	130858	NA	89.2	NA	NA	NA	NA	NA	NA	NA	89.3
Arabidopsis thaliana	AtH1	250103	NA	90.3	NA	NA	NA	NA	NA	NA	NA	90.7
Arabidopsis thaliana	Arabidopsis Tiling 1.0R Array	3130523	NA	15.7	NA	NA	NA	NA	NA	NA	NA	15.8
Bos taurus	Bovine	264126	58.3	50.4	43.9	31.1	35.9	27	NA	NA	NA	NA
Canis familiaris	CfCanine2	471650	38.6	2.3	50.8	46.6	53.2	38.9	NA	.1	NA	NA
Drosophila melanogaster	DmDrosophila2	262766	76	76.5	NA	73.4	76.4	72.3	NA	NA	NA	NA
Drosophila melanogaster	DmGenome1	195186	92.9	93.3	NA	92.4	93.2	90.6	NA	NA	NA	NA
Danio rerio	DrZebrafish	248013	54.4	56.7	39.6	34.6	38.6	32.4	NA	26.9	NA	NA
Gallus gallus	GgChicken	422825	52.9	14	43.1	38	43.4	32.1	NA	NA	NA	NA
Homo sapiens	Hs133A	246799	68.5	72.4	67.5	68	71.2	63.3	66.7	71.3	62.7	NA
Homo sapiens	Hs133Av2	246799	68.5	72.4	67.5	68	71.2	63.3	66.7	71.3	62.7	NA
Homo sapiens	Hs133B	248336	53.5	34.5	30.7	33	34.2	31.4	38.3	40.7	36.7	NA
Homo sapiens	Hs133P	603158	57.5	48.3	44.5	46	48.1	43.2	49.4	53	46.9	NA
Homo sapiens	Hs133X	672804	55.1	46.3	43.2	44.6	45.9	43.7	48.4	51.3	47.6	NA
Homo sapiens	Hs95Av2	197695	71	75.1	70.2	70.5	73.6	68.5	68.8	73.1	67	NA
Homo sapiens	HsEx10stv2	5383654	28.2	22	21.6	21.8	21.5	21.6	23.7	24.4	23.5	NA
Homo sapiens	HsFocus	97349	76.4	84.9	79.6	78.5	82.1	72.2	75.2	80.1	69.7	NA
Homo sapiens	HsNuGOHs1a520180	264407	69	69.9	65.6	69.7	72.6	65.7	65.6	69.6	62.2	NA
Homo sapiens	Chromosome 21/22 1.0 Array Set A	333692	1.4	.6	.6	.5	.5	.5	1.2	1.2	1.1	NA
Homo sapiens	Chromosome 21/22 1.0 Array Set B	333665	5.2	2.5	2.6	2.8	2.8	2.5	4.5	4.5	4.2	NA
Homo sapiens	Chromosome 21/22 1.0 Array Set C	334361	5.2	2.8	2.7	3	3	2.7	3.6	3.7	3.3	NA
Homo sapiens	Chromosome 21/22 2.0R Array	2243201	4.3	2.4	2.3	2.2	2.2	2.2	3.3	3.3	3.3	NA
Homo sapiens	ENCODE 2.0R Array	2214280	5.4	3.3	3	3.2	3.2	3.2	5.1	5.1	5.1	NA
Homo sapiens	Human Promoter 1.0R Array	4356207	9	5.1	4.9	4.8	4.9	4.5	5.7	5.9	5.4	NA
Homo sapiens	Human Tiling 1.0R Array Set 01	3104980	4.1	2.1	2	2.3	2.4	2.2	3.2	3.2	3	NA
Homo sapiens	Human Tiling 1.0R Array Set 02	3104956	2.9	1.3	1.3	1.2	1.2	1.1	.9	1	.8	NA
Homo sapiens	Human Tiling 1.0R Array Set 03	3104959	3.3	1.6	1.5	1.4	1.4	1.3	1.7	1.7	1.6	NA
Homo sapiens	Human Tiling 1.0R Array Set 04	3104968	2.5	1.2	1.1	1	1	.9	.8	.9	.8	NA
Homo sapiens	Human Tiling 1.0R Array Set 05	3104992	2.7	1.2	1.1	1.1	1.1	1	.9	.9	.8	NA
Homo sapiens	Human Tiling 1.0R Array Set 06	3104962	3.2	1.5	1.4	1.5	1.5	1.4	1.9	2	1.7	NA
Homo sapiens	Human Tiling 1.0R Array Set 07	3104969	2.7	1.3	1.2	1.2	1.2	1.1	1.4	1.7	1.3	NA
Homo sapiens	Human Tiling 1.0R Array Set 08	3105007	3.1	1.5	1.4	1.6	1.6	1.5	2.1	2.1	2	NA
Homo sapiens	Human Tiling 1.0R Array Set 09	3104992	3.7	1.8	1.8	1.8	1.8	1.7	1.2	1.3	1.1	NA
Homo sapiens	Human Tiling 1.0R Array Set 10	3104992	3.2	1.6	1.5	1.5	1.5	1.3	2	2	1.8	NA
Homo sapiens	Human Tiling 1.0R Array Set 11	3104964	3.8	1.9	1.8	1.7	1.7	1.5	2.4	2.4	2.2	NA
Homo sapiens	Human Tiling 1.0R Array Set 12	3104966	4.1	2.2	2.1	2	2	1.8	2.8	2.9	2.6	NA
Homo sapiens	Human Tiling 1.0R Array Set 13	3104957	4.5	2.7	2.6	2.6	2.6	2.4	3.5	3.5	3.2	NA
Homo sapiens	Human Tiling 1.0R Array Set 14	1487440	2.2	1.5	1.4	1.5	1.5	1.4	2.2	2.2	2.1	NA
Homo sapiens	Human Tiling 2.0R Array Set 01	6020961	3.7	1.9	1.8	2	2	1.8	2.7	2.7	2.5	NA
Homo sapiens	Human Tiling 2.0R Array Set 02	6190329	3.7	2	1.9	1.9	1.9	1.7	1.9	2	1.8	NA
Homo sapiens	Human Tiling 2.0R Array Set 03	6109114	3.1	1.6	1.6	1.5	1.5	1.4	2.2	2.2	2	NA
Homo sapiens	Human Tiling 2.0R Array Set 04	6199162	2.9	1.4	1.3	1.3	1.3	1.2	1.5	1.5	1.4	NA
Homo sapiens	Human Tiling 2.0R Array Set 05	6251118	3.1	1.5	1.4	1.4	1.4	1.2	1.4	1.7	1.3	NA
Homo sapiens	Human Tiling 2.0R Array Set 06	6124067	3.5	1.8	1.7	1.6	1.7	1.5	1.6	1.7	1.5	NA
Homo sapiens	Human Tiling 2.0R Array Set 07	6090639	3.6	1.8	1.8	1.8	1.8	1.6	2.5	2.5	2.3	NA
Macaca mulatta	Rhesus	667186	17.5	.6	48.2	36.3	37.1	34.4	NA	NA	NA	NA
Mus musculus	Mm11KsubA	130180	62.9	64.3	60.8	56.1	58.5	55	30.4	31.6	29.9	NA
Mus musculus	Mm11KsubB	118480	49.2	51.8	46.3	44.7	49.8	43.1	22.7	25.1	22	NA
Mus musculus	Mm430	495374	60.2	52.3	48.9	45.9	48.5	42.8	27.2	28.5	25.9	NA
Mus musculus	Mm430A	248864	72.9	73.3	68.8	65.1	69.2	60.3	35.2	37.2	33.2	NA
Mus musculus	Mouse Genome 430A 2.0	248864	72.9	73.3	68.8	65.1	69.2	60.3	35.2	37.2	33.2	NA
Mus musculus	Mm430B	247610	47.4	31.2	29	26.5	27.7	25.1	19.1	19.7	18.5	NA
Mus musculus	Mm74Av1	200641	56.2	56.3	52.8	49.3	52.4	47.5	26.4	27.8	25.7	NA
Mus musculus	Mm74Av2	196670	62.6	64.1	60.2	56.1	59.6	54.2	30.2	31.9	29.5	NA
Mus musculus	Mm74Bv2	195808	61.1	51.7	48.9	44.7	46.6	43.6	27.7	28.6	27.3	NA
Mus musculus	Mm74Cv2	181474	34.2	20.8	19.9	17.7	18.2	17.4	12.6	12.9	12.5	NA
Mus musculus	MmEx10stv1	4737634	27.9	22.4	22	21.2	21.3	20.9	13	13	12.9	NA
Mus musculus	MmNuGOMm1a520177	261635	65.4	64	60.2	58.5	61.9	54.2	30.5	32	28.7	NA
Mus musculus	Mouse Promoter 1.0R Array	4369636	7.9	5.1	4.9	4.4	4.5	4.1	3.1	3.1	2.9	NA
Mus musculus	Mouse Tiling 1.1R Array Set 01	3076926	2.9	1.7	1.6	1.4	1.4	1.3	.9	.9	.8	NA
Mus musculus	Mouse Tiling 1.1R Array Set 02	3161633	3.6	2.1	2.1	1.9	2	1.8	3	3	2.8	NA
Mus musculus	Mouse Tiling 1.1R Array Set 03	2534803	2.7	1.5	1.5	1.4	1.4	1.3	.8	.8	.8	NA
Mus musculus	Mouse Tiling 1.1R Array Set 04	2565519	3.2	1.9	1.9	1.8	1.8	1.6	2.6	2.6	2.5	NA
Mus musculus	Mouse Tiling 1.1R Array Set 05	3153176	1.8	1.8	1.3	1	1.2	.9	1.4	1.4	1.3	NA
Mus musculus	Mouse Tiling 1.1R Array Set 06	3166201	2.8	1.6	1.6	1.4	1.4	1.3	1.1	1.1	1	NA
Mus musculus	Mouse Tiling 1.1R Array Set 07	3123189	3.9	2.5	2.4	2.2	2.2	2	1	1	.9	NA
Mus musculus	Mouse Tiling 1.1R Array Set 08	3050130	2.7	1.4	1.4	1.3	1.3	1.1	.4	.4	.4	NA
Mus musculus	Mouse Tiling 1.1R Array Set 09	3155691	3.1	1.8	1.7	1.5	1.5	1.4	.4	.4	.4	NA
Mus musculus	Mouse Tiling 1.1R Array Set 10	3048063	3.1	1.8	1.8	1.6	1.6	1.4	.6	.6	.5	NA
Mus musculus	Mouse Tiling 1.1R Array Set 11	3167200	3.9	2.4	2.3	2.2	2.2	2	2.6	2.6	2.4	NA
Mus musculus	Mouse Tiling 1.1R Array Set 12	3165843	3.4	2.1	2	1.8	1.8	1.6	.5	.5	.5	NA
Mus musculus	Mouse Tiling 1.1R Array Set 13	3083184	2.7	1.5	1.4	1.3	1.3	1.2	.7	.7	.6	NA
Mus musculus	Mouse Tiling 1.1R Array Set 14	3146417	3.2	1.9	1.8	1.6	1.6	1.5	1	1	.9	NA
Mus musculus	Mouse Tiling 2.0R Array Set 01	5888394	3.3	1.9	1.8	1.6	1.6	1.5	.6	.6	.6	NA
Mus musculus	Mouse Tiling 2.0R Array Set 02	6098981	2.6	1.9	1.7	1.4	1.5	1.3	2.2	2.2	2.1	NA
Mus musculus	Mouse Tiling 2.0R Array Set 03	5883598	3	1.8	1.7	1.6	1.6	1.5	.8	.8	.7	NA
Mus musculus	Mouse Tiling 2.0R Array Set 04	5865723	3.6	2.2	2.2	2.1	2.1	1.9	2.5	2.5	2.3	NA
Mus musculus	Mouse Tiling 2.0R Array Set 05	5792498	2.9	1.7	1.7	1.5	1.5	1.3	.6	.7	.6	NA
Mus musculus	Mouse Tiling 2.0R Array Set 06	5888478	2.9	1.6	1.5	1.4	1.4	1.3	.8	.8	.8	NA
Mus musculus	Mouse Tiling 2.0R Array Set 07	5669507	2.7	1.6	1.5	1.4	1.4	1.2	.5	.5	.4	NA
Oryza sativa	OsRice	629427	NA	45.8	NA	NA	NA	NA	NA	NA	NA	NA
Pan troglodytes	Hs133A	246799	NA	72.8	49.5	46	49.6	41.5	NA	NA	NA	NA
Pan troglodytes	Hs133Av2	246799	NA	72.8	49.5	46	49.6	41.5	NA	NA	NA	NA
Pan troglodytes	Hs133B	248336	NA	33.2	27.6	20.6	21.9	18.9	NA	NA	NA	NA
Pan troglodytes	Hs133P	603158	NA	47.7	35	30.3	32.6	27.5	NA	NA	NA	NA
Pan troglodytes	Hs133X	672804	NA	45.7	33.7	28.6	30.3	27.7	NA	NA	NA	NA
Pan troglodytes	Hs95Av2	197695	NA	75.6	52.4	48	51.3	46	NA	NA	NA	NA
Pan troglodytes	HsEx10stv2	5383654	NA	21	18.6	16.2	16.4	15.4	NA	NA	NA	NA
Pan troglodytes	HsFocus	97349	NA	85.6	55.7	53	57.1	47	NA	NA	NA	NA
Pan troglodytes	HsNuGOHs1a520180	264407	NA	68.3	48.5	44.5	47.8	40.5	NA	NA	NA	NA
Pan troglodytes	Chromosome 21/22 1.0 Array Set A	333692	NA	.6	.6	.4	.4	.4	NA	NA	NA	NA
Pan troglodytes	Chromosome 21/22 1.0 Array Set B	333665	NA	2.5	2.4	1.8	1.8	1.5	NA	NA	NA	NA
Pan troglodytes	Chromosome 21/22 1.0 Array Set C	334361	NA	2.8	2.2	2	2	1.7	NA	NA	NA	NA
Pan troglodytes	Chromosome 21/22 2.0R Array	2243201	NA	2.3	1.9	1.5	1.6	1.5	NA	NA	NA	NA
Pan troglodytes	ENCODE 2.0R Array	2214280	NA	3.3	2.7	2.1	2.1	2.1	NA	NA	NA	NA
Pan troglodytes	Human Promoter 1.0R Array	4356207	NA	4.7	4.6	3.2	3.3	2.9	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 01	3104980	NA	2	1.9	1.5	1.5	1.3	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 02	3104956	NA	1.3	1.3	.9	1	.8	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 03	3104959	NA	1.5	1.4	1.1	1.1	.9	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 04	3104968	NA	1.1	1.1	.8	.8	.7	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 05	3104992	NA	1.1	1.1	.8	.8	.7	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 06	3104962	NA	1.4	1.3	1	1.1	.9	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 07	3104969	NA	1.3	1.3	.9	.9	.8	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 08	3105007	NA	1.5	1.4	1	1.1	.9	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 09	3104992	NA	1.7	1.7	1.2	1.3	1.1	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 10	3104992	NA	1.5	1.5	1.1	1.1	.9	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 11	3104964	NA	1.8	1.7	1.3	1.4	1.2	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 12	3104966	NA	2.1	2	1.5	1.5	1.3	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 13	3104957	NA	2.6	2.1	1.7	1.7	1.4	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 14	1487440	NA	1.5	1.2	.8	.8	.7	NA	NA	NA	NA
Pan troglodytes	Human Tiling 2.0R Array Set 01	6020961	NA	1.8	1.7	1.3	1.3	1.1	NA	NA	NA	NA
Pan troglodytes	Human Tiling 2.0R Array Set 02	6190329	NA	1.9	1.7	1.3	1.3	1.1	NA	NA	NA	NA
Pan troglodytes	Human Tiling 2.0R Array Set 03	6109114	NA	1.6	1.4	1	1.1	.9	NA	NA	NA	NA
Pan troglodytes	Human Tiling 2.0R Array Set 04	6199162	NA	1.3	1.3	1	1	.8	NA	NA	NA	NA
Pan troglodytes	Human Tiling 2.0R Array Set 05	6251118	NA	1.5	1.4	1	1	.9	NA	NA	NA	NA
Pan troglodytes	Human Tiling 2.0R Array Set 06	6124067	NA	1.7	1.6	1.2	1.2	1	NA	NA	NA	NA
Pan troglodytes	Human Tiling 2.0R Array Set 07	6090639	NA	1.7	1.7	1.2	1.3	1.1	NA	NA	NA	NA
Rattus norvegicus	Rn230	341459	64.5	45.9	40.3	31.8	33.8	28.6	NA	NA	NA	NA
Rattus norvegicus	Rn230A	174526	69.7	60.5	53.6	44	46.7	39.4	NA	NA	NA	NA
Rattus norvegicus	Rn230B	168033	59.2	30.8	26.6	19.1	20.3	17.5	NA	NA	NA	NA
Rattus norvegicus	Rn34A	139137	64.6	63.5	54.6	48.9	52.8	46.3	NA	NA	NA	NA
Rattus norvegicus	RnEx10stv1	4027776	23.5	22.8	21.5	21.6	21.6	21.3	NA	NA	NA	NA

Table 2. Target Count for Affymetrix and Custom Probe Sets

Species	Chip	Affy-UG1	Affy-ENSG2	Affy-REFSEQ3	UG	REFSEQ	ENTREZG	ENSG	ENST	ENSE	VEGAG	VEGAT	VEGAE	TAIR
Arabidopsis thaliana	AtGenome	1281	NA	7336	NA	8940	NA	NA	NA	NA	NA	NA	NA	7214
Arabidopsis thaliana	AtH1	NA	NA	21684	NA	25254	NA	NA	NA	NA	NA	NA	NA	21025
Arabidopsis thaliana	Arabidopsis Tiling 1.0R Array	NA	NA	NA	NA	15565	NA	NA	NA	NA	NA	NA	NA	13400
Bos taurus	Bovine	16306	5260	10373	11920	11289	9428	7493	10245	11245	NA	NA	NA	NA
Canis familiaris	CfCanine2	15542	16612	17002	12969	775	15771	16504	21922	31933	NA	58	NA	NA
Drosophila melanogaster	DmDrosophila2	NA	13636	13648	13490	19293	NA	13413	19099	20479	NA	NA	NA	NA
Drosophila melanogaster	DmGenome1	NA	12169	12208	12091	17582	NA	12103	17377	20475	NA	NA	NA	NA
Danio rerio	DrZebrafish	12459	5458	8575	8922	11587	6943	6071	8265	10092	NA	5264	NA	NA
Gallus gallus	GgChicken	17149	12172	12309	16872	3954	12495	11998	16530	23711	NA	NA	NA	NA
Homo sapiens	Hs133A	13103	11984	13280	11845	17531	11961	11834	23740	22299	13125	34000	29156	NA
Homo sapiens	Hs133Av2	13042	11984	13280	11845	17531	11961	11834	23740	22299	13125	34000	29156	NA
Homo sapiens	Hs133B	15217	6431	10492	10843	8729	6079	6290	11350	10709	7904	17156	15040	NA
Homo sapiens	Hs133P	29584	17322	20483	22182	25004	17527	17215	33977	34541	20083	51010	47113	NA
Homo sapiens	Hs133X	29475	17353	20609	21804	24755	17386	17031	32939	31612	19928	48516	42941	NA
Homo sapiens	Hs95Av2	7863	8297	9077	8159	12260	8135	8065	15996	14844	8929	22395	19335	NA
Homo sapiens	HsEx10stv2	NA	NA	NA	52928	35243	23851	26116	41624	232705	30839	84754	315922	NA
Homo sapiens	HsFocus	8068	7764	8494	7484	11530	7815	7676	14751	12015	8533	20711	15301	NA
Homo sapiens	HsNuGOHs1a520180	NA	NA	NA	16650	22669	16242	17158	29820	25957	18033	39305	31280	NA
Homo sapiens	Chromosome 21/22 1.0 Array Set A	NA	NA	NA	266	68	48	39	70	171	111	258	475	NA
Homo sapiens	Chromosome 21/22 1.0 Array Set B	NA	NA	NA	556	260	232	189	325	886	425	927	1792	NA
Homo sapiens	Chromosome 21/22 1.0 Array Set C	NA	NA	NA	529	250	165	177	293	905	256	428	1123	NA
Homo sapiens	Chromosome 21/22 2.0R Array	NA	NA	NA	1527	669	445	438	688	3358	756	1660	5707	NA
Homo sapiens	ENCODE 2.0R Array	NA	NA	NA	832	371	239	242	625	2709	458	1977	6200	NA
Homo sapiens	Human Promoter 1.0R Array	NA	NA	NA	16157	13943	9559	9207	17166	24131	10684	27462	35177	NA
Homo sapiens	Human Tiling 1.0R Array Set 01	NA	NA	NA	3754	1714	1125	999	2645	8602	1744	5703	13864	NA
Homo sapiens	Human Tiling 1.0R Array Set 02	NA	NA	NA	3076	997	666	595	996	4117	435	809	2949	NA
Homo sapiens	Human Tiling 1.0R Array Set 03	NA	NA	NA	3252	1096	726	625	1056	4814	809	2195	6701	NA
Homo sapiens	Human Tiling 1.0R Array Set 04	NA	NA	NA	2766	891	602	505	835	3380	378	866	2746	NA
Homo sapiens	Human Tiling 1.0R Array Set 05	NA	NA	NA	3129	935	619	518	946	3473	378	729	2466	NA
Homo sapiens	Human Tiling 1.0R Array Set 06	NA	NA	NA	3271	1244	815	728	1918	5531	1323	4343	7044	NA
Homo sapiens	Human Tiling 1.0R Array Set 07	NA	NA	NA	3106	1149	683	605	1004	3633	1089	2787	5210	NA
Homo sapiens	Human Tiling 1.0R Array Set 08	NA	NA	NA	3197	1169	773	737	1798	5593	1234	3390	7991	NA
Homo sapiens	Human Tiling 1.0R Array Set 09	NA	NA	NA	3636	1558	1033	971	1787	6096	676	2181	4974	NA
Homo sapiens	Human Tiling 1.0R Array Set 10	NA	NA	NA	3175	1200	821	723	1232	5059	1107	3113	7729	NA
Homo sapiens	Human Tiling 1.0R Array Set 11	NA	NA	NA	3716	1464	1072	898	1429	5963	1658	4059	12018	NA
Homo sapiens	Human Tiling 1.0R Array Set 12	NA	NA	NA	3986	1810	1220	1075	1669	6973	1865	5393	14763	NA
Homo sapiens	Human Tiling 1.0R Array Set 13	NA	NA	NA	4277	2218	1532	1505	2679	8684	2228	5412	12744	NA
Homo sapiens	Human Tiling 1.0R Array Set 14	NA	NA	NA	998	642	397	356	866	2501	737	1762	3875	NA
Homo sapiens	Human Tiling 2.0R Array Set 01	NA	NA	NA	6978	3005	2015	1789	4761	14412	3128	10290	21608	NA
Homo sapiens	Human Tiling 2.0R Array Set 02	NA	NA	NA	7154	3066	2151	2021	3685	12984	2168	5513	13814	NA
Homo sapiens	Human Tiling 2.0R Array Set 03	NA	NA	NA	6053	2617	1702	1546	2932	10120	2599	6762	16548	NA
Homo sapiens	Human Tiling 2.0R Array Set 04	NA	NA	NA	6282	2286	1511	1336	2454	8971	1816	4762	12884	NA
Homo sapiens	Human Tiling 2.0R Array Set 05	NA	NA	NA	6693	2623	1692	1508	2496	9275	1987	4689	11305	NA
Homo sapiens	Human Tiling 2.0R Array Set 06	NA	NA	NA	6867	2912	1929	1796	2897	10636	1666	5499	12457	NA
Homo sapiens	Human Tiling 2.0R Array Set 07	NA	NA	NA	7078	2945	2044	1782	3411	11725	3248	9494	22674	NA
Macaca mulatta	Rhesus	NA	NA	NA	5931	322	16002	13925	23940	29321	NA	NA	NA	NA
Mus musculus	Mm11KsubA	2149	4137	5186	4366	5675	4255	3994	5159	6049	2127	4836	4875	NA
Mus musculus	Mm11KsubB	2532	3063	3544	2768	3765	2833	2765	3709	5486	1367	3978	4520	NA
Mus musculus	Mm430	23598	15726	20500	19444	21561	16475	15768	21037	25438	7921	20174	20657	NA
Mus musculus	Mm430A	13395	11885	13568	12370	15534	12175	11723	15718	18765	5747	15036	14936	NA
Mus musculus	Mouse Genome 430A 2.0	13395	11885	13568	12370	15534	12175	11723	15718	18765	5747	15036	14936	NA
Mus musculus	Mm430B	13060	5494	11325	9327	7917	5716	5400	6878	7688	3425	6845	6737	NA
Mus musculus	Mm74Av1	8199	6964	8887	7318	9026	7004	6676	8707	10239	3383	8010	8045	NA
Mus musculus	Mm74Av2	8198	7712	9059	7786	9981	7737	7374	9621	11323	3753	8921	8961	NA
Mus musculus	Mm74Bv2	8701	5562	7818	7001	7233	5645	5295	6835	7899	3003	6677	6626	NA
Mus musculus	Mm74Cv2	6840	3519	6391	4502	3738	2721	2454	3084	3102	1644	3114	2878	NA
Mus musculus	MmEx10stv1	NA	NA	NA	38321	35232	24444	22927	30211	198757	12906	40421	162329	NA
Mus musculus	MmNuGOMm1a520177	NA	NA	NA	16349	20091	15415	15297	18866	20077	7580	15581	14472	NA
Mus musculus	Mouse Promoter 1.0R Array	NA	NA	NA	13892	14225	9881	9739	12482	21009	5009	13560	19411	NA
Mus musculus	Mouse Tiling 1.1R Array Set 01	NA	NA	NA	2230	1266	861	833	1082	4723	335	1177	3169	NA
Mus musculus	Mouse Tiling 1.1R Array Set 02	NA	NA	NA	2731	1650	1213	1201	1689	6609	1561	4532	11833	NA
Mus musculus	Mouse Tiling 1.1R Array Set 03	NA	NA	NA	1936	1087	760	725	907	3563	291	1102	2478	NA
Mus musculus	Mouse Tiling 1.1R Array Set 04	NA	NA	NA	2063	1322	916	900	1242	5023	1187	3286	8362	NA
Mus musculus	Mouse Tiling 1.1R Array Set 05	NA	NA	NA	1675	2844	1280	929	1328	3372	981	2193	4660	NA
Mus musculus	Mouse Tiling 1.1R Array Set 06	NA	NA	NA	2489	1471	1060	1001	1262	4772	525	1696	4295	NA
Mus musculus	Mouse Tiling 1.1R Array Set 07	NA	NA	NA	3182	2309	1657	1578	1970	7521	501	1806	4447	NA
Mus musculus	Mouse Tiling 1.1R Array Set 08	NA	NA	NA	2200	1180	836	842	1039	4403	206	727	1810	NA
Mus musculus	Mouse Tiling 1.1R Array Set 09	NA	NA	NA	2488	1391	985	980	1228	5187	172	662	1744	NA
Mus musculus	Mouse Tiling 1.1R Array Set 10	NA	NA	NA	2479	1420	1027	1001	1255	5559	211	889	2408	NA
Mus musculus	Mouse Tiling 1.1R Array Set 11	NA	NA	NA	3086	1875	1365	1331	1915	8107	1361	3830	10615	NA
Mus musculus	Mouse Tiling 1.1R Array Set 12	NA	NA	NA	2718	1785	1228	1198	1534	6313	236	861	2131	NA
Mus musculus	Mouse Tiling 1.1R Array Set 13	NA	NA	NA	2247	1219	855	839	1047	4262	266	964	2521	NA
Mus musculus	Mouse Tiling 1.1R Array Set 14	NA	NA	NA	2626	1591	1129	1091	1406	5652	409	1693	4307	NA
Mus musculus	Mouse Tiling 2.0R Array Set 01	NA	NA	NA	4758	2723	1906	1862	2367	10392	437	1544	4344	NA
Mus musculus	Mouse Tiling 2.0R Array Set 02	NA	NA	NA	4091	4293	2344	1975	2819	9305	2457	6388	15802	NA
Mus musculus	Mouse Tiling 2.0R Array Set 03	NA	NA	NA	4781	3064	2156	2053	2556	9822	704	2552	6205	NA
Mus musculus	Mouse Tiling 2.0R Array Set 04	NA	NA	NA	5272	3428	2409	2344	3308	13775	2507	6922	18635	NA
Mus musculus	Mouse Tiling 2.0R Array Set 05	NA	NA	NA	4404	2591	1810	1769	2258	9311	498	2017	5224	NA
Mus musculus	Mouse Tiling 2.0R Array Set 06	NA	NA	NA	4513	2556	1820	1767	2197	9012	634	2332	6337	NA
Mus musculus	Mouse Tiling 2.0R Array Set 07	NA	NA	NA	4117	2352	1676	1594	2010	8714	426	1312	3390	NA
Oryza sativa	OsRice	23634	NA	2339	NA	24015	NA	NA	NA	NA	NA	NA	NA	NA
Pan troglodytes	Hs133A	NA	NA	NA	NA	17603	10628	10213	16710	16213	NA	NA	NA	NA
Pan troglodytes	Hs133Av2	NA	NA	NA	NA	17603	10628	10213	16710	16213	NA	NA	NA	NA
Pan troglodytes	Hs133B	NA	NA	NA	NA	7906	6328	5077	7581	7307	NA	NA	NA	NA
Pan troglodytes	Hs133P	NA	NA	NA	NA	23944	15906	14862	24024	24863	NA	NA	NA	NA
Pan troglodytes	Hs133X	NA	NA	NA	NA	23695	15549	14362	22860	23135	NA	NA	NA	NA
Pan troglodytes	Hs95Av2	NA	NA	NA	NA	12400	7307	6869	10965	11029	NA	NA	NA	NA
Pan troglodytes	HsEx10stv2	NA	NA	NA	NA	25954	24675	20457	31837	175435	NA	NA	NA	NA
Pan troglodytes	HsFocus	NA	NA	NA	NA	11827	6716	6489	9964	8515	NA	NA	NA	NA
Pan troglodytes	HsNuGOHs1a520180	NA	NA	NA	NA	21542	14715	14050	20382	18112	NA	NA	NA	NA
Pan troglodytes	Chromosome 21/22 1.0 Array Set A	NA	NA	NA	NA	52	52	41	66	152	NA	NA	NA	NA
Pan troglodytes	Chromosome 21/22 1.0 Array Set B	NA	NA	NA	NA	249	211	143	253	703	NA	NA	NA	NA
Pan troglodytes	Chromosome 21/22 1.0 Array Set C	NA	NA	NA	NA	229	172	166	260	665	NA	NA	NA	NA
Pan troglodytes	Chromosome 21/22 2.0R Array	NA	NA	NA	NA	613	520	429	685	2996	NA	NA	NA	NA
Pan troglodytes	ENCODE 2.0R Array	NA	NA	NA	NA	358	309	238	414	2047	NA	NA	NA	NA
Pan troglodytes	Human Promoter 1.0R Array	NA	NA	NA	NA	11797	9672	7876	12268	16748	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 01	NA	NA	NA	NA	1327	1270	969	1868	5903	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 02	NA	NA	NA	NA	725	767	566	855	3340	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 03	NA	NA	NA	NA	794	827	600	965	3941	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 04	NA	NA	NA	NA	627	686	486	724	2632	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 05	NA	NA	NA	NA	669	737	504	763	2721	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 06	NA	NA	NA	NA	908	910	666	1215	3832	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 07	NA	NA	NA	NA	880	893	589	941	3040	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 08	NA	NA	NA	NA	960	945	665	1327	3741	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 09	NA	NA	NA	NA	1212	1185	871	1488	4551	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 10	NA	NA	NA	NA	910	892	674	1124	4093	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 11	NA	NA	NA	NA	1123	1112	832	1297	4969	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 12	NA	NA	NA	NA	1366	1384	1041	1594	5536	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 13	NA	NA	NA	NA	1994	1709	1430	2269	6140	NA	NA	NA	NA
Pan troglodytes	Human Tiling 1.0R Array Set 14	NA	NA	NA	NA	633	527	335	561	1437	NA	NA	NA	NA
Pan troglodytes	Human Tiling 2.0R Array Set 01	NA	NA	NA	NA	2281	2234	1687	3168	9845	NA	NA	NA	NA
Pan troglodytes	Human Tiling 2.0R Array Set 02	NA	NA	NA	NA	2507	2426	1908	3053	9549	NA	NA	NA	NA
Pan troglodytes	Human Tiling 2.0R Array Set 03	NA	NA	NA	NA	2232	1997	1468	2384	7463	NA	NA	NA	NA
Pan troglodytes	Human Tiling 2.0R Array Set 04	NA	NA	NA	NA	1719	1753	1274	2013	6972	NA	NA	NA	NA
Pan troglodytes	Human Tiling 2.0R Array Set 05	NA	NA	NA	NA	1957	2006	1451	2228	7320	NA	NA	NA	NA
Pan troglodytes	Human Tiling 2.0R Array Set 06	NA	NA	NA	NA	2310	2206	1661	2602	8564	NA	NA	NA	NA
Pan troglodytes	Human Tiling 2.0R Array Set 07	NA	NA	NA	NA	2250	2176	1606	2763	8805	NA	NA	NA	NA
Rattus norvegicus	Rn230	23331	9405	14279	18641	18670	11498	10034	13439	14339	NA	NA	NA	NA
Rattus norvegicus	Rn230A	12982	7102	10490	10873	13167	8619	7543	10067	10248	NA	NA	NA	NA
Rattus norvegicus	Rn230B	12162	3143	6852	9068	7549	3923	3226	4229	4470	NA	NA	NA	NA
Rattus norvegicus	Rn34A	5050	3994	5205	4676	5744	4224	3935	5718	7469	NA	NA	NA	NA
Rattus norvegicus	RnEx10stv1	NA	NA	NA	31406	36595	21280	21901	31601	192279	NA	NA	NA	NA

Table 3. Affy vs Custom

Cdf	Species	Chip	Affy Only	Custom Only	Shared	Percentage of identical probesets in shared targets	Percentage of probesets with difference<=25% in shared targets	Percentage of probesets with difference>50% in all targets
ENSG	Bos taurus	Bovine	1198	3431	4062	20	71.2	56.7
ENSG	Canis familiaris	CfCanine2	1086	978	15526	18.2	78.5	15.5
ENSG	Drosophila melanogaster	DmDrosophila2	287	64	13349	66.7	99.1	2.7
ENSG	Drosophila melanogaster	DmGenome1	174	108	11995	92.5	99.1	2.5
ENSG	Danio rerio	DrZebrafish	1542	2155	3916	18.1	81.9	50.8
ENSG	Gallus gallus	GgChicken	1184	1010	10988	20.7	77.8	20.1
ENSG	Homo sapiens	Hs133A	678	528	11306	42.1	91.2	11.4
ENSG	Homo sapiens	Hs133Av2	678	528	11306	42.1	91.2	11.4
ENSG	Homo sapiens	Hs133B	525	384	5906	50.6	91.2	14.6
ENSG	Homo sapiens	Hs133P	970	863	16352	39	90.4	11.8
ENSG	Homo sapiens	Hs133X	1112	790	16241	49.7	90.6	12.2
ENSG	Homo sapiens	Hs95Av2	528	296	7769	48.3	91	11.5
ENSG	Homo sapiens	HsFocus	430	342	7334	50.2	93.5	10.6
ENSG	Mus musculus	Mm11KsubA	322	179	3815	39.6	88	14.8
ENSG	Mus musculus	Mm11KsubB	446	148	2617	19.8	75.2	25.4
ENSG	Mus musculus	Mm430	866	908	14860	40.6	89.4	12.3
ENSG	Mus musculus	Mm430A	716	554	11169	41.4	90.7	11.9
ENSG	Mus musculus	Mouse Genome 430A 2.0	716	554	11169	41.4	90.7	11.9
ENSG	Mus musculus	Mm430B	547	453	4947	51.6	90.1	18.3
ENSG	Mus musculus	Mm74Av1	679	391	6285	43.1	88.2	17.2
ENSG	Mus musculus	Mm74Av2	748	410	6964	38.3	80.8	18
ENSG	Mus musculus	Mm74Bv2	527	260	5035	44.9	86.5	16.6
ENSG	Mus musculus	Mm74Cv2	1241	176	2278	37.3	70.3	44.7
ENSG	Rattus norvegicus	Rn230	753	1382	8652	35.3	86.4	22.1
ENSG	Rattus norvegicus	Rn230A	507	948	6595	40.3	90.3	19.7
ENSG	Rattus norvegicus	Rn230B	473	556	2670	34.2	83.3	30.5
ENSG	Rattus norvegicus	Rn34A	346	287	3648	22.7	83	18.2
ENTREZG	Bos taurus	Bovine	2737	1157	8271	30.3	73.1	37.1
ENTREZG	Canis familiaris	CfCanine2	1426	190	15581	17.7	74.3	14.1
ENTREZG	Danio rerio	DrZebrafish	5367	2165	4778	16.9	75.9	64.7
ENTREZG	Gallus gallus	GgChicken	1612	1792	10703	19.4	66.5	30.3
ENTREZG	Homo sapiens	Hs133A	1707	244	11717	37.8	82.3	17.6
ENTREZG	Homo sapiens	Hs133Av2	1707	244	11717	37.8	82.3	17.6
ENTREZG	Homo sapiens	Hs133B	4812	211	5868	35	65.5	51.5
ENTREZG	Homo sapiens	Hs133P	3797	417	17110	25.2	60.7	29.7
ENTREZG	Homo sapiens	Hs133X	4091	449	16937	32.6	62.5	30.6
ENTREZG	Homo sapiens	Hs95Av2	1175	171	7964	44.8	83.8	18
ENTREZG	Homo sapiens	HsFocus	825	132	7683	49.7	92.3	12.3
ENTREZG	Mus musculus	Mm11KsubA	1245	126	4129	38.8	84.6	29.2
ENTREZG	Mus musculus	Mm11KsubB	858	122	2711	20.1	71.9	34.2
ENTREZG	Mus musculus	Mm430	5957	444	16031	29.9	67.3	34.9
ENTREZG	Mus musculus	Mm430A	1941	269	11906	38.3	82.6	18.7
ENTREZG	Mus musculus	Mouse Genome 430A 2.0	1941	269	11906	38.3	82.6	18.7
ENTREZG	Mus musculus	Mm430B	7115	269	5447	37.4	66.6	61.7
ENTREZG	Mus musculus	Mm74Av1	2331	214	6790	39.2	77.2	31.9
ENTREZG	Mus musculus	Mm74Av2	1775	229	7508	37.5	75.4	26.1
ENTREZG	Mus musculus	Mm74Bv2	2738	206	5439	39.5	74.3	40.3
ENTREZG	Mus musculus	Mm74Cv2	4252	161	2560	31.5	58	69.4
ENTREZG	Rattus norvegicus	Rn230	3369	573	10925	28.9	66.9	33.4
ENTREZG	Rattus norvegicus	Rn230A	2315	430	8189	38.1	80.9	28.2
ENTREZG	Rattus norvegicus	Rn230B	3238	308	3615	33	69.7	54.2
ENTREZG	Rattus norvegicus	Rn34A	1155	156	4068	22.4	77.6	29.4
REFSEQ	Arabidopsis thaliana	AtGenome	1373	2977	5963	75.3	96.9	42.5
REFSEQ	Arabidopsis thaliana	AtH1	3863	7433	17821	90.6	98.8	38.9
REFSEQ	Bos taurus	Bovine	3006	3922	7367	50	76.7	51.3
REFSEQ	Canis familiaris	CfCanine2	16483	256	519	56.8	72.8	97.1
REFSEQ	Drosophila melanogaster	DmDrosophila2	3346	8991	10302	95.6	98.6	54.6
REFSEQ	Drosophila melanogaster	DmGenome1	3107	8481	9101	93.4	98.7	56.1
REFSEQ	Danio rerio	DrZebrafish	3369	6381	5206	42.8	83.3	67.1
REFSEQ	Gallus gallus	GgChicken	8703	348	3606	52	74.2	72.4
REFSEQ	Homo sapiens	Hs133A	4797	9048	8483	55.9	84.8	63.1
REFSEQ	Homo sapiens	Hs133Av2	4797	9048	8483	55.9	84.8	63.1
REFSEQ	Homo sapiens	Hs133B	6082	4319	4410	44.8	68.1	72.6
REFSEQ	Homo sapiens	Hs133P	7893	12414	12590	37.4	63.9	65.4
REFSEQ	Homo sapiens	Hs133X	8161	12307	12448	41.3	65.4	66
REFSEQ	Homo sapiens	Hs95Av2	3412	6595	5665	58	86.1	65
REFSEQ	Homo sapiens	HsFocus	2991	6027	5503	67.7	93.3	62.6
REFSEQ	Mus musculus	Mm11KsubA	1958	2448	3227	52.6	85.9	60
REFSEQ	Mus musculus	Mm11KsubB	1394	1615	2150	40.8	76.4	61.9
REFSEQ	Mus musculus	Mm430	8790	9851	11710	44.8	69.7	64
REFSEQ	Mus musculus	Mm430A	4262	6228	9306	59.2	84.7	54.2
REFSEQ	Mus musculus	Mouse Genome 430A 2.0	4262	6228	9306	59.2	84.7	54.2
REFSEQ	Mus musculus	Mm430B	8055	4647	3270	46.3	68.4	81.2
REFSEQ	Mus musculus	Mm74Av1	3555	3694	5332	54.5	79.4	59.9
REFSEQ	Mus musculus	Mm74Av2	3164	4086	5895	51.6	77.5	57.6
REFSEQ	Mus musculus	Mm74Bv2	4052	3467	3766	47.1	75.4	68.9
REFSEQ	Mus musculus	Mm74Cv2	4743	2090	1648	32.8	58.7	83.7
REFSEQ	Oryza sativa	OsRice	406	22082	1933	NA	4.3	99
REFSEQ	Rattus norvegicus	Rn230	7425	11816	6854	47.2	70	75.7
REFSEQ	Rattus norvegicus	Rn230A	4803	7480	5687	59.5	82.6	69.4
REFSEQ	Rattus norvegicus	Rn230B	5376	6073	1476	44.2	72.8	89.6
REFSEQ	Rattus norvegicus	Rn34A	1820	2359	3385	53.5	81.8	57.7
UG	Bos taurus	Bovine	5069	683	11237	52.3	86.5	35.7
UG	Canis familiaris	CfCanine2	6872	4299	8670	34.2	70.1	58.1
UG	Danio rerio	DrZebrafish	4878	1341	7581	34.2	83	47.9
UG	Gallus gallus	GgChicken	6677	6400	10472	35	74	58.2
UG	Homo sapiens	Hs133A	2212	954	10891	42.6	81.2	26.2
UG	Homo sapiens	Hs133Av2	2192	995	10850	42.6	81.3	26.4
UG	Homo sapiens	Hs133B	6303	1929	8914	51.6	82.6	50.4
UG	Homo sapiens	Hs133P	10153	2751	19431	41.7	78.1	43.4
UG	Homo sapiens	Hs133X	10389	2718	19086	45	77.7	44.3
UG	Homo sapiens	Hs95Av2	1264	1560	6599	45.1	80.1	34.7
UG	Homo sapiens	HsFocus	1138	554	6930	52.8	89.9	21.6
UG	Mus musculus	Mm11KsubA	518	2735	1631	41.1	80.6	69.3
UG	Mus musculus	Mm11KsubB	560	796	1972	29.7	75.2	46.4
UG	Mus musculus	Mm430	5863	1709	17735	47.1	81	33.3
UG	Mus musculus	Mm430A	1819	794	11576	49.9	83.8	21.6
UG	Mus musculus	Mouse Genome 430A 2.0	1819	794	11576	49.9	83.8	21.6
UG	Mus musculus	Mm430B	5039	1306	8021	54.3	84.4	46.1
UG	Mus musculus	Mm74Av1	2233	1352	5966	48.5	79.6	41.9
UG	Mus musculus	Mm74Av2	1606	1194	6592	47.8	81.6	34.2
UG	Mus musculus	Mm74Bv2	2477	777	6224	46.2	82	38
UG	Mus musculus	Mm74Cv2	2989	651	3851	41.7	75.9	53.1
UG	Rattus norvegicus	Rn230	5993	1303	17338	57.5	88.2	31.3
UG	Rattus norvegicus	Rn230A	2868	759	10114	61	89	27.9
UG	Rattus norvegicus	Rn230B	3760	666	8402	58.6	90.2	35.9
UG	Rattus norvegicus	Rn34A	1050	676	4000	43.9	79.1	34.8

1. Identical probe sets are those with identical probe contents in Affymetrix annotation and the custome annotation.
2. Since most probe level data analysis algorithms have built mechanism for dealing with outliers, probe sets that differ only a couple of probes from the Affymetrix probe sets should have similar probe set level signal values.
3. These are probe sets that are supposed to represent the same target but there are >=50% probe content difference between the Affymetrix and custom probe set definition.

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